Welcome to Fusion Cancer

Next-generation mRNA sequencing (RNA-seq) has long been recognized as an effcient tool in dynamic transcriptome analysis. It can provide not only an increased base coverage, but also a higher sample throughput. It facilitates the ability to search for alternative-spliced transcripts, post-transcriptional modifications, gene fusions, mutations/SNPs and changes in gene expression. Many databases have been set up for fusion gene detection research, such as Mitelman Database of Chromosome Aberration and Gene Fusions in Cancer and ChimerDB. But they are derived either from experiments or transcript sequences, containing limited records. The huge amount of RNA-seq data produced in the past few years provides abundant resources in fusion gene detection. So we can use these RNA-seq data in the Sequence Read Archive (SRA) on NCBI to look for fusion genes in human cancer genome.

Introduction to fusion genes.


Fusion genes are chimeric genes formed by two previously separated genes. They may be the products of chromosome structure changes such as insertion, deletion, inversion and translocation. Fusion genes can be divided into two types: inter-chromosomal fusion genes and intra-chromosomal fusion genes. Inter-chromosomal fusion genes are generated by genes of two different chromosomes, while intra-chromosomal fusion genes are formed by genes from the same chromosome.

Fusion genes are known as drivers of some cancers, such as hematological cancers, sarcomas, and prostate cancer, so it can serve as a biomarker for cancer treatment. In the past, chromosome banding analysis, fluorescence in situ hybridization (FISH) and reverse transcription polymerase chain reaction (RT-PCR) have been used to detect fusion genes. But now next-generation sequencing (NGS) bears significant advantages in fusion gene detection.

Links in red, green and blue stand for fusion genes in Class A, B and C respectively, where Recurrent rate >= 0.3 for prostate cancer and >= 0.4 for other cancers. The definition of each Class has been fully described in Help page.

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